Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1655

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 861

Length: 1436
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.23

Warning! 58 characters in sequence are not A, C, G, or T


Found at i:189 original size:3 final size:3

Alignment explanation


    Indices: 181--275  Score: 70
    Period size: 3  Copynumber: 30.7  Consensus size: 3

        171 AAGCTATTAT

                                                *                          
        181 ATA ATA ATA ATA ATA ATA CGATA AGTA ACA ATA AT- ATAA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA --ATA A-TA ATA ATA ATA AT-A ATA ATA ATA

            *                *                                *    *     
        229 TTA ATA ATA ATA ACA ATA ATGA A-A GATA ATA AT- ATA TTA AAA ATA
          1 ATA ATA ATA ATA ATA ATA AT-A ATA -ATA ATA ATA ATA ATA ATA ATA

              
        274 AT
          1 AT

        276 GAGGAAAATA


Statistics
Matches: 73,  Mismatches: 10, Indels: 18
        0.72            0.10        0.18

Matches are distributed among these distances:
   2    5  0.07
   3   57  0.78
   4    8  0.11
   5    3  0.04

ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31


Consensus pattern (3 bp):   
ATA

Found at i:678 original size:3 final size:3

Alignment explanation


    Indices: 670--764  Score: 70
    Period size: 3  Copynumber: 30.7  Consensus size: 3

        660 AAGCTATTAT

                                                *                          
        670 ATA ATA ATA ATA ATA ATA CGATA AGTA ACA ATA AT- ATAA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA --ATA A-TA ATA ATA ATA AT-A ATA ATA ATA

            *                *                                *    *     
        718 TTA ATA ATA ATA ACA ATA ATGA A-A GATA ATA AT- ATA TTA AAA ATA
          1 ATA ATA ATA ATA ATA ATA AT-A ATA -ATA ATA ATA ATA ATA ATA ATA

              
        763 AT
          1 AT

        765 GAGGAAAATA


Statistics
Matches: 73,  Mismatches: 10, Indels: 18
        0.72            0.10        0.18

Matches are distributed among these distances:
   2    5  0.07
   3   57  0.78
   4    8  0.11
   5    3  0.04

ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31


Consensus pattern (3 bp):   
ATA

Done.